EQ (equalization) can be a very useful tool. When used correctly, it can flesh out the inadequacies in your sound, help make up for deficiencies in an amplifier rig or PA system, even compensate for bad acoustics in your performance space. It can also, when not utilized properly, muddy or distort your sound, add noise, and compromise the dynamic range available to you. It is important to think about how or why you might use it, and just where in your signal chain would be the best place for it to be used.
At its most basic level, EQ is a form of controlled distortion. It enables you to affect a specified range of your signal, letting you boost or cut one realm of frequencies, while having a minimal effect on others. Initially, this seems like a great idea, and here is often where trouble starts. Because of the nature of EQ, its use can cause phase problems, add noise to the signal, and reduce the available dynamic range in some cases. A number of acoustic preamps these days have an EQ section built in, ranging from fairly simple shelving types to more complex parametric or semi-parametric types, allowing the user wider control over the affected frequencies.
The downsides here are that you don't get this power for free. Because of the nature of these units, they generate noise along with the boost or cut to the signal they provide. Since the signal from your guitar at this point is pretty low compared to the finished signal that goes to your system's power amps, the noise that is generated here is amplified as well on its journey, translating to an audible (and annoying) hiss or hum by the time it comes out of the speakers. These units are often battery powered as well, which limits just how much a signal can be amplified before it runs out of clean amplification (headroom). Boosting the EQ can eat up the available headroom and compromise the dynamic range to the point where playing too forcefully can inadvertently clip your system. The amplifying components in these type of systems often are noisier as well, because they are chosen to promote longer battery life instead of lower noise or distortion. The result? You turn up the EQ, and hiss noticeably increases.
So, given these problems, what might help?
AC powered units tend to have much better noise and distortion specs, partly due to a larger power supply to allow them more headroom, and usually a better set of components that can take advantage of this increased headroom. Many mixers have an insert point on their input channels, and this can be an ideal point to add your EQ using a send/return cable made for this purpose. Looking deeper here, the best solution is to use as little EQ as possible. Ideally, the EQ should be needed sparingly, sort of as the icing on the cake, not as a much needed tool just to obtain a useable sound. Often in recording studios, engineers will use microphone selection, placement techniques and instrument selection to create the desired sound, using EQ as a last resort if all else fails. The same should be true of a well-designed acoustic guitar system. Using pickup selection, judicious placement, and of course, proper instrument selection will go a very long way towards getting that finished sound that you want to present to your listening audience.